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- PDB-2h2p: Crystal structure of CLC-ec1 in complex with Fab fragment in SeCN- -

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Basic information

Entry
Database: PDB / ID: 2h2p
TitleCrystal structure of CLC-ec1 in complex with Fab fragment in SeCN-
Components
  • CLC Cl transporter
  • FAB fragment, heavy chain
  • FAB fragment, light chain
KeywordsION TRANSPORT / CLC / transporter / chloride / antiport
Function / homology
Function and homology information


chloride:proton antiporter activity / cellular stress response to acidic pH / voltage-gated chloride channel activity / immunoglobulin complex, circulating / chloride transmembrane transport / proton transmembrane transport / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response ...chloride:proton antiporter activity / cellular stress response to acidic pH / voltage-gated chloride channel activity / immunoglobulin complex, circulating / chloride transmembrane transport / proton transmembrane transport / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / blood microparticle / extracellular exosome / identical protein binding / plasma membrane
Similarity search - Function
Clc chloride channel / Clc chloride channel / Chloride channel, ClcA / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype ...Clc chloride channel / Clc chloride channel / Chloride channel, ClcA / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
SELENOCYANATE ION / H(+)/Cl(-) exchange transporter ClcA / Ighg protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsNguitragool, W. / Miller, C.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Uncoupling of a CLC Cl(-)/H(+) Exchange Transporter by Polyatomic Anions
Authors: Nguitragool, W. / Miller, C.
History
DepositionMay 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CLC Cl transporter
B: CLC Cl transporter
C: FAB fragment, heavy chain
D: FAB fragment, light chain
E: FAB fragment, heavy chain
F: FAB fragment, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,72214
Polymers192,8826
Non-polymers8408
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)220.581, 121.578, 151.240
Angle α, β, γ (deg.)90.000, 128.250, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ARG / End label comp-ID: ALA / Refine code: 3 / Auth seq-ID: 18 - 454 / Label seq-ID: 18 - 454

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe complex is a homodimer of chains A and B along with nonequivalent Fab fragments

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Components

#1: Protein CLC Cl transporter / ClC-ec1 / H(+)/Cl(-) exchange transporter clcA


Mass: 49658.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: clcA, eriC / Production host: Escherichia coli (E. coli) / References: UniProt: P37019
#2: Antibody FAB fragment, heavy chain


Mass: 23693.918 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: Hybridoma Cell line / References: UniProt: Q4VBH1*PLUS
#3: Antibody FAB fragment, light chain


Mass: 23088.443 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: Hybridoma Cell line
#4: Chemical
ChemComp-SEK / SELENOCYANATE ION


Mass: 104.977 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CNSe

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.13 Å3/Da / Density % sol: 70.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM KSCN, PEG 300 38%, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.98 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 61583 / % possible obs: 98.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.087 / Χ2: 2.973 / Net I/σ(I): 12.5
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.652 / Num. unique all: 5821 / Χ2: 1.13 / % possible all: 93.8

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3.1 Å37.67 Å
Translation3.1 Å37.67 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→50 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.901 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.856 / ESU R Free: 0.439 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28 2834 5 %RANDOM
Rwork0.278 ---
all0.2781 56530 --
obs0.2781 56530 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.512 Å2
Baniso -1Baniso -2Baniso -3
1--5.65 Å20 Å2-6.99 Å2
2--7.97 Å20 Å2
3----10.97 Å2
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13223 0 8 0 13231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02213553
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.96218456
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.41451743
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.23222.985479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.87152145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0851567
X-RAY DIFFRACTIONr_chiral_restr0.0940.22121
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0210087
X-RAY DIFFRACTIONr_nbd_refined0.3320.27367
X-RAY DIFFRACTIONr_nbtor_refined0.3420.29547
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.2590
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2930.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2580.22
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1748TIGHT POSITIONAL0.060.05
1524LOOSE POSITIONAL0.215
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 217 -
Rwork0.422 3859 -
obs-4076 97.16 %

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